Due to torrential rains making the pitch unplayable, they played the 2007–2008 season in the Delta State town of Oghara. During the 2008–09 season, Bayelsa was forced to play three home games in Ibadan after crowd trouble in their derby with Ocean Boys. Then at the new year's break the team was suspended from continuing their league schedule despite being at the top of the table. This was due to outstanding debts and salaries. In a surprising move, the team sacked technical adviser Miekeme Fekete right as the squad was traveling to Brazzaville to play in the CAF Confederation Cup. They won the Nigerian Premier Leaguefor the first time after a 2–2 draw at Warri Wolves F.C. on June 14, qualifying them for the 2010 CAF Champions League. The celebration was dampened however when captain Abel Tador was killed by robbers hours after the game.
2009/10 season
In January 2010, the Bayelsa State government said they were looking for private sponsorship to take over the team. They were relegated at the end of the season by one point after losing three of their last four games and being banished to play home games in Kano. They protested the relegation, claiming three points should have been awarded from an abandoned game in Bauchi when home team Wikki Tourists left the pitch. After months of court action, their relegation was confirmed in September 2010.
2011 season
Financial problems plagued Bayelsa's return to the second division. They let many players leave on free transfers at the start of the season due to non-payment of salaries. In May 2011, they boycotted their state FA cup final and had a protest at the Bayelsa State government building because of non-payment, in some cases going back two years to their league title. At the time, they were at the top of the table in the National League Division 1-B.
2012 season
They won their nine-team division to win promotion back to the Premier League and placed second to rivals Nembe City F.C. in the Nigerian National League Super Four tournament. They were relegated after a last place finishin 2015.